Mercurial > repos > lecorguille > xcms_plot_chromatogram

annotate xcms_plot_chromatogram.xml @ 10:dbd877060ac3 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
author workflow4metabolomics
date Wed, 12 Feb 2020 08:30:06 -0500
parents 0290cd6b3354
children 37d31fd64eb4
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dbd877060ac3 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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1 <tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@TOOL_VERSION@.0">
0
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2 <description>Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s)</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 <import>macros_xcms.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <expand macro="stdio"/>
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11 <command><![CDATA[
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12 @COMMAND_RSCRIPT@//xcms_plot_chromatogram.r
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14 images 'c("${"\",\"".join(map(str, $images))}")'
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16 #if str($sampleMetadata) != 'None':
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17 sampleMetadata '$sampleMetadata'
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18 #end if
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20 @COMMAND_FILE_LOAD@
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21 ]]></command>
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23 <inputs>
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24 <param name="images" type="data" format="rdata.msnbase.raw,rdata.xcms.findchrompeaks,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks or adjustRtime" multiple="true" />
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25 <param name="sampleMetadata" label="Sample metadata file " format="tabular" type="data" optional="true" help="Must contain at least one column with the sample id and one column with the sample class"/>
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27 <expand macro="input_file_load"/>
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28 </inputs>
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30 <outputs>
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31 <data name="ticsPdf" format="pdf" label="TICs.pdf" from_work_dir="TICs.pdf"/>
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32 <data name="bpisPdf" format="pdf" label="BPIs.pdf" from_work_dir="BPIs.pdf" />
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33 </outputs>
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35 <tests>
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36 <test>
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37 <param name="images" value="faahKO-single.xset.merged.group.retcor.RData" ftype="rdata"/>
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38 <expand macro="test_file_load_single"/>
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39 <param name="sampleMetadata" value="sampleMetadata.tab" ftype="tabular"/>
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40 <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="5000" />
dbd877060ac3 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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41 <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="5000" />
0
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42 </test>
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43 <!-- DISABLE FOR TRAVIS
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44 <test>
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45 <param name="images" value="ko15-raw.RData,ko16-raw.RData,wt15-raw.RData,wt16-raw.RData" ftype="rdata"/>
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46 <expand macro="test_file_load_single"/>
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47 <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" />
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48 <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" />
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49 </test>
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50 -->
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51 </tests>
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52
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53 <help><![CDATA[
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55 @HELP_AUTHORS@
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56
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57 ======================
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58 xcms plot chromatogram
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59 ======================
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60
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61 -----------
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62 Description
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63 -----------
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65 This tool will plot Base Peak Intensity chromatogram (BPI) and Total Ion Current chromatogram (TIC) from xcms experiments.
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66
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68 -----------------
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69 Workflow position
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70 -----------------
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72 **Upstream tools**
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74 =========================== ======================== ==============================
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75 Name Output file Format
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76 =========================== ======================== ==============================
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77 MSnbase.readMSData ``*``.raw.RData rdata.msnbase.raw
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78 --------------------------- ------------------------ ------------------------------
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79 xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
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80 --------------------------- ------------------------ ------------------------------
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81 xcms.findChromPeaks Merger xset.merged.RData rdata.xcms.retcor
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82 --------------------------- ------------------------ ------------------------------
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83 xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor
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84 =========================== ======================== ==============================
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85
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86 .. image:: xcms_plot_chromatogram_workflow.png
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88 ---------------------------------------------------
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90 ------------
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91 Output files
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92 ------------
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93
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94 **Total Ion Current (TIC) chromatogram**
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95 | Sum of intensity (Y) of all ions detected at each retention time (X)
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96
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97 **Base Peak Intensity Chromatogram (BPI)**
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98 | Sum of intensity (Y) of the most intense peaks at each retention time (X)
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99
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100 ---------------------------------------------------
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101
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102 Changelog/News
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103 --------------
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104
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105 .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS
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106
10
dbd877060ac3 "planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f1caf2a3bf23cf319a75dd12c86402555dd02617"
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107 @HELP_XCMS_NEWVERSION_3610@
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108
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109 @HELP_XCMS_NEWVERSION_3440@
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110
0
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111 **Version 3.0.0.0 - 07/03/2018**
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112
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113 - NEW: This new tool will plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience. It will replace those created by xcmsSet and retcor tools.
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114
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115 ]]></help>
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116
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117 <expand macro="citation" />
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118 </tool>